EP4306657A1

EP4306657A1 - Composition for diagnosing pancreatic cancer

Info

Publication number: EP4306657A1
Application number: EP22767462.9A
Authority: EP
Inventors: Hyung-Keun Lee; Dong-Ki Lee; So-Young Kim; Sung-Ill JANG
Original assignee: Acurasysbio Co Ltd
Current assignee: Acurasysbio Co Ltd
Priority date: 2021-03-08
Filing date: 2022-03-08
Publication date: 2024-01-17
Also published as: WO2022191566A1; US20240142456A1; KR20220126661A

Abstract

The present invention relates to a composition, a kit, and a method of providing information for diagnosis, which are capable of diagnosing pancreatic cancer and capable of diagnosing pancreatic cancer by distinguishing it from other pancreatic diseases or other cancer types.

Description

Technical Field

The present invention relates to a composition and a kit for diagnosing pancreatic cancer, and a method of providing information for diagnosis of pancreatic cancer.

Background Art

Studies on methods for treating and diagnosing cancer among major diseases in modern people have been relatively actively conducted, focusing on lung cancer, liver cancer, gastric cancer, etc., which occur at high incidence. However, studies on esophageal cancer, colorectal cancer, pancreatic cancer, etc., which occur at low incidence, are relatively insufficient.
In particular, pancreatic cancer does not show recognizable symptoms in its early stages, and usually shows symptoms such as pain and weight loss after systemic metastasis has already occurred, indicating that the cure rate of pancreatic cancer is relatively low. Thus, regular testing for pancreatic cancer is very important. Most of the clinical symptoms of pancreatic cancer gradually appear, and frail health, loss of appetite, and weight loss are the most common symptoms. Pancreatic cancer is a fatal cancer with a 5-year survival rate of 1 to 4% and a median survival period of 5 months, and has the poorest prognosis among human cancers. In addition, since 80 to 90% of pancreatic cancer patients are diagnosed in a state in which curative resection making a cure possible is not possible, the prognosis thereof is poor. Also, the treatment of pancreatic cancer mainly depends on chemotherapy. Thus, there is a more urgent need to develop an early diagnosis method for pancreatic cancer than any other human cancer.
Several anticancer drugs, including 5-fluorouracil, gemcitabine, and Tarceva, which are known to be effective for pancreatic cancer until now, have extremely low therapeutic effects, and the response rate to chemotherapy using these drugs is only 15%. This fact suggests that the development of a more effective early diagnosis method and treatment method for pancreatic cancer is urgently required in order to improve the prognosis of pancreatic cancer patients. Appropriate diagnosis and treatment of precursor lesions of pancreatic cancer, which are at a stage prior to progression to fatal pancreatic cancer, is very important to improve pancreatic cancer treatment results.
For the diagnosis of pancreatic cancer or precursor lesions of pancreatic cancer, blood test (CA19-9), gastro-duodenography with X-ray, cholangiography through the skin and liver, and retrograde endoscopic cholangiography are used. Although disease lesions have been detected by these methods, ultrasonography and computed tomography have recently been most commonly used. Relatively accurate test results may be obtained by performing a more precise biopsy. However, this diagnostic method has low accuracy, or subjects are unwilling to undergo the diagnostic method because the diagnostic method is inconvenient and painful. Therefore, there has been a demand for the development of a test method capable of diagnosing pancreatic cancer or precursor lesions of pancreatic cancer conveniently and rapidly.
Korean Patent No. 10-0819122 and Korean Patent Application Publication No. 2012-0082372 disclose technologies using various pancreatic cancer markers, including matrilin, transthyretin, stratifin, and the like. However, diagnostic efficiency and accuracy significantly differ between markers. Therefore, there is a need to discover more effective markers and develop a diagnostic method using the same.

DISCLOSURE

Technical Problem

An object of the present invention is to provide a composition for diagnosing pancreatic cancer.
Another object of the present invention is to provide a kit for diagnosing pancreatic cancer.
Still another object of the present invention is to provide a method of providing information for diagnosis of pancreatic cancer.
However, objects to be achieved by the present invention are not limited to the above-mentioned objects, and other objects not mentioned herein will be clearly understood by those skilled in the art from the following description.

Technical Solution

One embodiment of the present invention is directed to a biomarker for diagnosing cancer comprising either at least one protein selected from the group consisting of PLD4 (phospholipase D family member 4), NR4A1 (nuclear receptor subfamily 4 group A member 1), KLRF1 (killer cell lectin like receptor F1), and ID3 (inhibitor of DNA binding 3, HLH protein), or a gene encoding the at least one protein.
In the present invention, the "PLD4 (phospholipase D family member 4)" is 5'-3' exonuclease PLD4, which degrades single-stranded DNA (ssDNA). The PLD4 functions to regulate an inflammatory cytokine response by reducing the concentration of ssDNA that stimulates TLR9 through nucleic acid degradation, and is known to be involved in phagocytosis of activated microglia. The PLD4 protein may consist of the amino acid sequence represented by SEQ ID NO: 1, without being limited thereto.
In the present invention, the "NR4A1 (nuclear receptor subfamily 4 group A member 1)" is also known as NGFIB (nerve growth factor IB) or Nur77, belongs to the family of intracellular transcription factors, and is known to be involved in cell cycle regulation, inflammation, or apoptosis. The NR4A1 may consist of the amino acid sequence represented by SEQ ID NO: 2, without being limited thereto.
In the present invention, the "KLRF1 (killer cell lectin like receptor F1)" is expressed in natural killer cells and is known to be involved in cytotoxicity and cytokine secretion. The KLRF1 may consist of the amino acid sequence represented by SEQ ID NO: 3, without being limited thereto.
In the present invention, the "ID3 (inhibitor of DNA binding 3, HLH protein)" is a helix-loop-helix (HLH) protein that forms a heterodimer with other HLH proteins. The ID3 protein lacks a DNA binding domain and thus inhibits the binding of other HLH proteins to DNA. The ID3 may consist of the amino acid sequence represented by SEQ ID NO: 4, without being limited thereto.
In the present invention, the biomarker may further comprise IL7R (interleukin 7 receptor) protein or a gene encoding the same.
In the present invention, the "IL7R (interleukin 7 receptor)" is a protein found on the cell surface, is made up of two different protein chains that form a heterodimer, and is composed of two subunits, CD127 and CD132. The IL7R is observed in various cells, including various naive and memory T cells, and is known to play an important role in the development of immune cells. The IL7R may consist of the amino acid sequence represented by SEQ ID NO: 5, without being limited thereto.
In one example of the present invention, the biomarker may comprise PLD4 and ID3, without being limited thereto.
In another example of the present invention, the biomarker may comprise PLD4, ID3 and IL7R, without being limited thereto.
In still another example of the present invention, the biomarker may comprise PLD4, ID3, NR4A1 and KLRF1, without being limited thereto.
In yet another example of the present invention, the biomarker may comprise PLD4, ID3, NR4A1, KLRF1 and IL7R, without being limited thereto.
In the present invention, the expression level of the biomarker, etc. may be measured from a biological sample isolated from a subject of interest, preferably a liquid biopsy, for example, blood, serum or plasma, or cells or exosomes isolated from the liquid biopsy.
In the present invention, the term "subject of interest" refers to individuals that have cancer or are highly likely to have cancer, wherein the individuals may be mammals, including humans. For example, the subject of interest may be selected from the group consisting of humans, rats, mice, guinea pigs, hamsters, rabbits, monkeys, dogs, cats, cows, horses, pigs, sheep, and goats, and is preferably a human, without being limited thereto.
In the present invention, when the expression level of the biomarker according to the present invention in a liquid biopsy isolated from a subject of interest or in cells or exosomes isolated from the liquid biopsy is measured, there is no need for an invasive process such as subjecting the patient to laparotomy and isolating tissue cells from tissue (e.g., pancreatic tissue), it takes less than about 5 minutes to obtain the biopsy, and it takes about less than 2 hours to measure the expression levels of the various disease biomarkers according to the present invention from the biopsy, suggesting that whether the disease has occurred or the likelihood of occurrence of the disease may be determined very rapidly and conveniently.
In the present invention, the term "cancer" refers to or describes the physiological condition typically characterized by unregulated cell growth in a mammal. The cancer may be thyroid cancer, parathyroid cancer, gastric cancer, ovarian cancer, colorectal cancer, pancreatic cancer, liver cancer, breast cancer, cervical cancer, lung cancer, non-small cell lung cancer, prostate cancer, gallbladder cancer, bile duct cancer, non-Hodgkin's lymphoma, Hodgkin's lymphoma, hematological cancer, bladder cancer, kidney cancer, melanoma, colon cancer, bone cancer, skin cancer, head cancer, uterine cancer, rectal cancer, brain tumor, perianal cancer, fallopian tube carcinoma, endometrial carcinoma, vaginal cancer, vulvar carcinoma, esophageal cancer, small intestine cancer, endocrine adenocarcinoma, adrenal cancer, soft tissue sarcoma, urethral cancer, penile cancer, cancer of ureter, renal cell carcinoma, renal pelvic carcinoma, central nervous system (CNS) tumor, primary CNS lymphoma, spinal cord tumor, brainstem glioma, or pituitary adenoma. Preferably, the cancer may be pancreatic cancer, but is not limited thereto and may be any type of cancer whose progression (such as tumor differentiation and/or proliferation) is dependent on the cancer cells or cancer stem cells described in the present invention.
In the present invention, the term "pancreatic cancer" refers to cancer originating from pancreatic cells. There are several types of pancreatic cancer, but pancreatic ductal adenocarcinomas originating from pancreatic ductal cells account for about 90%, and thus pancreatic cancer generally refers to pancreatic ductal adenocarcinoma. In addition, there are cystic cancer (cystadenocarcinoma), endocrine tumors, and the like. About 5% to 10% of pancreatic cancer patients have a genetic predisposition, and about 7.8% of pancreatic cancer patients have a family history of pancreatic cancer, which is higher than the incidence of pancreatic cancer in the general population (0.6%). Pancreatic cancer is a cancer with a very poor prognosis, with a 5-year survival rate of 5% or less. This is because most cases are diagnosed after the cancer has progressed, and thus cases in which surgical resection is possible at the time of diagnosis are less than 20%, and even if the tumor has been completely resected when viewed visually, there is little improvement in survival rate due to micrometastasis, and the responsiveness of the cancer to chemotherapy and radiotherapy is low. Therefore, the most important method to improve the survival rate is early detection and surgical removal of the cancer when there are no symptoms or nonspecific symptoms.
In the present invention, the term "diagnosis" means identifying the presence or characteristics of a pathological condition. For the purposes of the present invention, the term "diagnosis" may mean predicting the likelihood of occurrence, growth, progression, or metastasis of cancer, or may mean distinguishing cancer from other diseases, for example, a pancreatic disease, in particular, pancreatitis (including both acute and chronic), pancreatic benign tumors (lipoma or intraductal papillary mucinous neoplasm (IPMN), etc.), or may mean distinguishing between cancer types, particularly, distinguishing pancreatic cancer from other cancer types.
In the present invention, the term "pancreatitis" refers to diseases caused by inflammation of the pancreas, and includes acute pancreatitis and chronic pancreatitis. Pancreatic juice contains digestive enzymes such as amylase (which hydrolyzes carbohydrates), trypsin (which hydrolyzes proteins), and lipase (which hydrolyzes fats). Pancreatitis is not only caused by autolysis of the pancreas by the enzymes because pancreatic juice does not flow smoothly due to alcohol abuse, gallstones, etc., but also caused by various factors such as metabolic disorders, drugs, and abdominal damage. Pancreatitis is an inflammatory disease of the pancreas that causes pancreatic acinar cell damage, extensive interstitial edema, hemorrhage, and migration of neutrophilic granulocytes to the site of injury. Pancreatitis can be broadly divided into two types: mild type pancreatitis in which interstitial edema and peripancreatic fat necrosis are found; and severe type pancreatitis accompanied by extensive peri pancreatic and intrapancreatic fat necrosis, pancreatic parenchymal necrosis, and hemorrhage.
Another embodiment of the present invention is directed to a composition for diagnosing cancer containing, as an active ingredient, an agent for measuring the expression level of at least one protein selected from the group consisting of PLD4, NR4A1, KLRF1, and ID3, or a gene encoding the at least one protein.
In the present invention, the composition for diagnosing may further contain an agent for measuring the expression level of IL7R protein or a gene encoding the same.
In one example of the present invention, the composition for diagnosing may contain, as an active ingredient, an agent for measuring the expression levels of PLD4 and ID3 proteins or genes encoding the same, without being limited thereto.
In another example of the present invention, the composition for diagnosing may contain, as an active ingredient, an agent for measuring the expression levels of PLD4, ID3 and IL7R proteins or genes encoding the same, without being limited thereto.
In still another example of the present invention, the composition for diagnosing may contain, as an active ingredient, an agent for measuring the expression levels of PLD4, ID3, NR4A1 and KLRF1 proteins or genes encoding the same, without being limited thereto.
In yet another example of the present invention, the composition for diagnosing may contain, as an active ingredient, an agent for measuring the expression levels of PLD4, ID3, NR4A1, KLRF1 and IL7R proteins or genes encoding the same, without being limited thereto.
In the present invention, the agent for measuring the expression level of the protein may comprise at least one from the group consisting of an antibody, an oligopeptide, a ligand, a peptide nucleic acid (PNA), and an aptamer, which bind specifically to the protein, without being limited thereto.
In the present invention, the "antibody" refers to a substance that specifically binds to an antigen and causes an antigen-antibody reaction. For the purposes of the present invention, the antibody refers to an antibody that specifically binds to the protein. Examples of the antibody of the present invention include all of polyclonal antibodies, monoclonal antibodies, and recombinant antibodies. This antibody may be readily produced using techniques well known in the art. For example, a polyclonal antibody may be produced by a method well known in the art, which includes a process of obtaining a serum containing the antibody by injecting the antigen of the protein into an animal and collecting blood from the animal. This polyclonal antibody may be produced from any animal such as goat, rabbit, sheep, monkey, horse, pig, cow, dog, or the like. In addition, a monoclonal antibody may be produced using the hybridoma method well known in the art (see Kohler and Milstein (1976) European Journal of Immunology 6:511-519), or the phage antibody library technology (see Clackson et al, Nature, 352:624-628, 1991; Marks et al, J. Mol. Biol., 222:58, 1-597, 1991). The antibody produced by the above method may be isolated and purified using a method such as gel electrophoresis, dialysis, salt precipitation, ion exchange chromatography, or affinity chromatography. In addition, examples of the antibody of the present invention include not only a complete form having two full-length light chains and two full-length heavy chains, but also functional fragments of an antibody molecule. The phrase "functional fragment of an antibody molecule" refers to a fragment having at least an antigen-binding function, and examples of the fragment include Fab, F(ab'), F(ab')2, Fv, and the like.
In the present invention, the "oligopeptide" is a peptide composed of 2 to 20 amino acids and examples thereof include, but are not limited to, a dipeptide, tripeptide, tetrapeptide, and pentapeptide.
In the present invention, the term "PNA (Peptide Nucleic Acid)" refers to an artificially synthesized DNA or RNA-like polymer, which was first introduced by the Professors Nielsen, Egholm, Berg and Buchardt at University of Copenhagen, Denmark in 1991. DNA has a phosphate-ribose sugar backbone, but PNA has repeated N-(2-aminoethyl)-glycine backbones linked via peptide bonds, and thus has a significantly increased binding affinity for DNA or RNA and significantly increased stability. Thus, the PNA is used for molecular biology, diagnostic assays and antisense therapies. The PNA is disclosed in detail in the literature [Nielsen P E, Egholm M, Berg R H, Buchardt O (December 1991). "Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide". Science 254(5037): 1497-1500].
In the present invention, the term "aptamer" refers to an oligonucleotide or a peptide molecule, and general contents regarding the aptamer are disclosed in detail in the literature [Bock L C et al., Nature 355(6360):5646(1992); Hoppe-Seyler F, Butz K "Peptide aptamers: powerful new tools for molecular medicine". J Mol Med. 78(8):42630(2000); Cohen B A, Colas P, Brent R. "An artificial cell-cycle inhibitor isolated from a combinatorial library". Proc Natl Acad Sci USA. 95(24): 142727(1998)].
In the present invention, the agent for measuring the expression level of the gene encoding the protein may comprise at least one selected from the group consisting of a primer, a probe, and an antisense nucleotide, which bind specifically to the gene encoding the protein, without being limited thereto.
In the present invention, the term "primer" refers to a fragment that recognizes a target gene sequence. The primer comprises a pair of forward and reverse primers, but is preferably a pair of primers providing analysis results with specificity and sensitivity. When the nucleic acid sequence of the primer is a sequence inconsistent with the non-target sequence present in the sample, and thus is a primer that amplifies only the target gene sequence containing the complementary primer binding site without inducing nonspecific amplification, high specificity may be imparted.
In the present invention, the term "probe" refers to a substance capable of binding specifically to a target substance to be detected in a sample, and refers to a substance capable of specifically detecting the presence of the target substance in the sample through the binding. The type of probe is not particularly limited so long as it is commonly used in the art. Preferably, the probe may be PNA (peptide nucleic acid), LNA (locked nucleic acid), a peptide, a polypeptide, a protein, RNA or DNA. Most preferably, the probe is PNA. More specifically, the probe is a biomolecule derived from an organism or an analogue thereof, or is produced in vitro. Examples of the probe include an enzyme, a protein, an antibody, a microorganism, an animal and/or plant cell and organ, a neuron, DNA, and RNA. Examples of the DNA include cDNA, genomic DNA, and an oligonucleotide, examples of the RNA include genomic RNA, mRNA and an oligonucleotide, and examples of the protein include antibodies, antigens, enzymes, peptides, and the like.
In the present invention, the term "LNA (locked nucleic acid)" refers to a nucleic acid analogue containing a 2'-O or 4'-C methylene bridge [J Weiler, J Hunziker and J Hall Gene Therapy (2006) 13, 496.502]. LNA nucleosides comprise the common bases of DNA and RNA, and can form base pairs according to the Watson-Crick base-pair rule. However, LNA fails to form an ideal shape in the Watson-Crick bond due to "locking" of the molecule attributable to the methylene bridge. When LNA is incorporated in a DNA or RNA oligonucleotide, it can more rapidly pair with a complementary nucleotide chain, thus increasing the stability of the double strand.
In the present invention, the term "antisense" means an oligomer that has a nucleotide sequence and a backbone between subunits, wherein an antisense oligomer is hybridized with the target sequence in the RNA by Watson-Crick base pairing to typically allow the formation of the mRNA and RNA:oligomer heterodimers with the mRNA in the target sequence. The oligomer may have an accurate or approximate sequence complementarity to the target sequence.
Information on the PLD4, NR4A1, KLRF1, ID3 and IL7R proteins or the genes encoding these proteins according to the present invention is known. Thus, based on this information, any person skilled in the art will be able to easily design primers, probes or antisense nucleotides that bind specifically to the genes encoding the proteins.
In the present invention, the expression levels of the PLD4, NR4A1, KLRF1, ID3 and IL7R proteins or the genes encoding the same may be measured from a biological sample isolated from a subject of interest, preferably a liquid biopsy, for example, blood, serum or plasma, or cells or exosomes isolated from the liquid biopsy.
In the present invention, the cancer may be thyroid cancer, parathyroid cancer, gastric cancer, ovarian cancer, colorectal cancer, pancreatic cancer, liver cancer, breast cancer, cervical cancer, lung cancer, non-small cell lung cancer, prostate cancer, gallbladder cancer, bile duct cancer, non-Hodgkin's lymphoma, Hodgkin's lymphoma, hematological cancer, bladder cancer, kidney cancer, melanoma, colon cancer, bone cancer, skin cancer, head cancer, uterine cancer, rectal cancer, brain tumor, perianal cancer, fallopian tube carcinoma, endometrial carcinoma, vaginal cancer, vulvar carcinoma, esophageal cancer, small intestine cancer, endocrine adenocarcinoma, adrenal cancer, soft tissue sarcoma, urethral cancer, penile cancer, cancer of ureter, renal cell carcinoma, renal pelvic carcinoma, central nervous system (CNS) tumor, primary CNS lymphoma, spinal cord tumor, brainstem glioma, or pituitary adenoma. Preferably, the cancer may be pancreatic cancer, but is not limited thereto and may be any type of cancer whose progression (such as tumor differentiation and/or proliferation) is dependent on the cancer cells or cancer stem cells described in the present invention.
In the present invention, the composition for diagnosing may be used to predict the likelihood of occurrence, growth, progression, or metastasis of cancer, or may be used to distinguish cancer from other diseases, for example, a pancreatic disease, in particular, pancreatitis (including both acute and chronic), pancreatic benign tumors (lipoma or intraductal papillary mucinous neoplasm (IPMN), etc.), or may be used to diagnose pancreatic cancer by distinguishing between cancer types, particularly, distinguishing pancreatic cancer from other cancer types.
Still another embodiment of the present invention is directed to a kit for diagnosing cancer comprising the composition for diagnosing of the present invention.
In the present invention, the term "kit" refers to a tool in which a probe or antibody that binds specifically to a biomarker component is labeled with a detectable substance so that the expression level of the biomarker may be assessed. The kit may include not only a direct label that directly labels a substance capable of being detected with respect to a probe or antibody by a reaction with a substrate, but also an indirect label to which a marker that develops color by a reaction with another reagent, which is directly-labeled, is conjugated. The kit may comprise a chromogenic substrate solution to induce a chromogenic reaction with the label, a washing liquid, and other solutions, and may be prepared to comprise reagent components used. In the present invention, the kit may be a kit comprising essential components necessary for performing RT-PCR, and may comprise, in addition to each primer pair specific for the marker gene, a test tube, a reaction buffer, deoxynucleotides (dNTPs), Taq-polymerase, reverse transcriptase, DNase and RNase inhibitors, sterile water, and the like. The kit may also be a kit for detecting genes for cancer diagnosis comprising essential components necessary for performing DNA chip assay. The DNA chip kit may comprise a substrate to which a cDNA corresponding to a gene or a fragment thereof is attached as a probe, wherein the substrate may comprise a cDNA corresponding to a quantitative control gene or a fragment thereof. The kit of the present invention is not limited thereto and may be any type of kit known in the art.
In the present invention, the kit may be an RT-PCR kit, a DNA chip kit, an ELISA kit, a protein chip kit, a rapid kit, or a multiple reaction monitoring (MRM) kit.
The kit of the present invention may further include a composition, solution or device consisting of one or more types of different components, suitable for an analysis method. For example, the kit of the present invention may further include essential elements required for a reverse transcription polymerase chain reaction (RT-PCR). A kit for RT-PCR includes a primer pair specific for a marker protein-coding gene. The primers are nucleotides having a sequence specific for the nucleic acid sequence of the gene, having a length of approximately 7 bp to 50 bp, and more preferably, approximately 10 bp to 30 bp. In addition, the primers may include a primer specific for the nucleic acid sequence of a control gene. Alternatively, the kit for RT-PCR may include a test tube or another suitable container, a reaction buffer solution (pH and magnesium concentrations vary), deoxynucleotides (dNTPs), enzymes such as Taq-polymerase and reverse transcriptase, DNase, RNase inhibitor DEPC-water, and distilled water.
In addition, the kit of the present invention may include essential elements required for a DNA chip. The DNA chip kit may include a substrate to which cDNA or an oligonucleotide, which corresponds to a gene or a fragment thereof, is attached, and a reagent, agent and enzymes for preparing a fluorescence-labeled probe. In addition, the substrate may include cDNA or an oligonucleotide, which corresponds to a control gene or a fragment thereof, is attached.
In addition, the kit for diagnosing cancer according to the present invention may comprise essential components required for performing ELISA. The ELISA kit comprises an antibody specific to the protein. The antibody is a monoclonal antibody, a polyclonal antibody or a recombinant antibody, which has a high specificity and affinity for the marker protein and shows little or no cross-reactivity with other proteins. Also, the ELISA kit may comprise an antibody specific to a control protein. In addition, the ELISA kit may comprise reagents capable of detecting bound antibodies, for example labelled secondary antibodies, chromophores, enzymes (e.g., conjugated with antibodies) and the substrates thereof or other substances which are capable of binding to antibodies.
As a support for antigen-antibody interactions in the kit, a nitrocellulose membrane, a PVDF membrane, well plate synthesized of a polyvinyl resin or a polystyrene resin, or a slide glass formed of glass may be used, but the present invention is not limited thereto.
In addition, in the kit of the present invention, a label for a secondary antibody is preferably a conventional chromophore that develops color, and preferably, labels such as fluorescein or a dye such as poly L-lysine-fluorescein isothiocyanate (FITC), or rhodamine-B-isothiocyanate (RITC), horseradish peroxidase (HRP), alkaline phosphatase, colloidal gold, may be used, but the present invention is not limited thereto.
In addition, a chromogenic substrate for inducing color development in the kit of the present invention is preferably used according to a label that develops color, and may be 3,3',5,5'-tetramethyl benzidine (TMB), 2,2'-azino-bis(3-ethylbenzothiazolin-6-sulfonic acid) (ABTS) or o-phenylenediamine (OPD). Here, the chromogenic substrate is more preferably provided in a state of being dissolved in a buffer solution (0.1 M NaAc, pH 5.5). A chromogenic substrate such as TMB may be decomposed by HRP used as a label of a secondary antibody conjugate to generate a chromogenic deposit, and by visually observing the degree of deposition of the chromogenic deposit, the presence of the marker proteins is detected.
In the present invention, the washing solution preferably contains a phosphate buffer solution, NaCl, and Tween 20, and is more preferably a buffer solution (PBST) composed of a 0.02 M phosphate buffer solution, 0.13 M NaCl, and 0.05% Tween 20. After the secondary antibody is allowed to react with the antigen-antibody conjugate after the antigen-antibody binding reaction, a proper amount of the washing solution is added to the support to wash the support 3 to 6 times. A sulfuric acid (H₂SO₄) solution may be preferably used as the reaction stop solution.
Yet another embodiment of the present invention is directed to a method of providing information for diagnosis of cancer, the method comprising a step of measuring the expression level of at least one protein selected from the group consisting of PLD4, NR4A1, KLRF1 and ID3, or a gene encoding the at least one protein, in a biological sample isolated from a subject of interest.
In the present invention, the term "subject of interest" refers to individuals that have cancer or are highly likely to have cancer, wherein the individuals may be mammals, including humans. For example, the subject of interest may be selected from the group consisting of humans, rats, mice, guinea pigs, hamsters, rabbits, monkeys, dogs, cats, cows, horses, pigs, sheep, and goats, and is preferably a human, without being limited thereto.
In the present invention, the term "biological sample" refers to any substance, biological body fluid, tissue or cells obtained from or derived from the subject. The biological sample may be at least one selected from the group consisting of whole blood, leukocytes, peripheral blood mononuclear cells, buffy coat, plasma, serum, sputum, tears, mucus, nasal washes, nasal aspirate, breath, urine, semen, saliva, peritoneal washings, ascites, cystic fluid, meningeal fluid, amniotic fluid, glandular fluid, pancreatic fluid, lymph fluid, pleural fluid, nipple aspirate, bronchial aspirate, synovial fluid, joint aspirate, organ secretions, cells, cell extracts, and cerebrospinal fluid. Preferably, the biological sample may be cells or exosomes isolated from a liquid biopsy such as blood, serum or plasma.
In the present invention, the method of providing information may further comprise a step of measuring the expression level of IL7R protein or a gene encoding the same in the biological sample isolated from the subject of interest.
In one example of the present invention, the method of providing information may comprise a step of measuring the expression levels of PLD4 and ID3 proteins or genes encoding the same in the biological sample isolated from the subject of interest, without being limited thereto.
In another example of the present invention, the method of providing information may comprise a step of measuring the expression levels of PLD4, ID3 and IL7R proteins or genes encoding the same in the biological sample isolated from the subject of interest, without being limited thereto.
In still another example of the present invention, the method of providing information may comprise a step of measuring the expression levels of PLD4, ID3, NR4A1 and KLRF1 proteins or genes encoding the same in the biological sample isolated from the subject of interest, without being limited thereto.
In yet another example of the present invention, the method of providing information may comprise a step of measuring the expression levels of PLD4, ID3, NR4A1, KLRF1 and IL7R proteins or genes encoding the same in the biological sample isolated from the subject of interest, without being limited thereto.
In the present invention, the agent for measuring the expression level of the protein may comprise at least one from the group consisting of an antibody, an oligopeptide, a ligand, a peptide nucleic acid (PNA), and an aptamer, which bind specifically to the protein.
In the present invention, measurement of the expression level of the protein may be performed by protein chip assay, immunoassay, ligand binding assay, MALDI-TOF (Matrix Assisted Laser Desorption/Ionization Time of Flight) mass spectrometry, SELDI-TOF (Surface Enhanced Laser Desorption/Ionization Time of Flight) mass spectrometry, radioimmunoassay, radial immunodiffusion, Ouchterlony immunodiffusion, Rocket immunoelectrophoresis, immunohistostaining, complement fixation test, 2-D electrophoresis, liquid chromatography-mass spectrometry (LC-MS), liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS), Western blotting, or enzyme-linked immunosorbent assay (ELISA).
In the present invention, measurement of the expression level of the protein may be performed by a multiple reaction monitoring (MRM) method.
In the present invention, in the multiple reaction monitoring method, either a synthetic peptide obtained by substituting a specific amino acid of a target peptide with an isotope or E. coli beta-galactosidase may be used as an internal standard.
In the present invention, the agent for measuring the expression level of the gene encoding the protein may comprise at least one selected from the group consisting of a primer, a probe, and an antisense nucleotide, which bind specifically to the gene encoding the protein.
In the present invention, measurement of the expression level of the gene encoding the protein may be performed by reverse transcription polymerase reaction (RT-PCR), competitive RT-PCR, real-time RT-PCR, RNase protection assay (RPA), Northern blotting, or DNA chip assay.
In the method of providing information according to the present invention, details regarding the antibody, oligopeptide, ligand, peptide nucleic acid (PNA), aptamer, etc., and details regarding the primer, probe, etc. overlap with those described above, and thus the detailed description thereof will be omitted below to avoid undue complexity of the specification.
In the present invention, when the expression level of at least one protein selected from the group consisting of PLD4, NR4A1 and KLRF1, or the gene encoding the at least one protein, measured in the biological sample isolated from the subject of interest, is lower than a control, it may be predicted that cancer has occurred or is highly likely to occur cancer in the subject of interest.
In the present invention, when the expression level of at least one protein selected from among ID3 and IL7R, or the gene encoding the at least one protein, measured in the biological sample isolated from the subject of interest, is higher than a control, it may be predicted that cancer has occurred or is highly likely to occur cancer in the subject of interest.
In the present invention, the term "control" may be, but is not limited to, the expression level of the corresponding biomarker protein or the gene encoding the protein in a healthy normal control group, or the average or median value of the expression level of the corresponding marker protein or the gene encoding the same in biological samples derived from patients with pancreatic disease, or the average value or median value of the expression level of the corresponding marker protein or the gene encoding the same in biological samples derived from cancer patients, preferably from patients with cancer types other than pancreatic cancer.
In the present invention, the method of providing information may further comprise a step of substituting, into Equation 1 below, the expression levels of PLD4, NR4A1, KLRF1, ID3 and IL7R proteins or the genes encoding the proteins, measured in the biological sample isolated from the subject of interest:

$A = a 1 - b 1 X (PLD 4) - c 1 X (NR 4 A 1) - d 1 X (KLRF 1) + e 1 X (IL) (7 R) + f 1 X$

wherein

al is a rational number of 1.5 to 2.0, preferably 1.75 to 2.0;
b1 is a rational number of 0.1 to 0.3, preferably 0.15 to 0.25;
c1 is a rational number of 0.01 to 0.03, preferably 0.02 to 0.03;
d1 is a rational number of 0.005 to 0.02, preferably 0.01 to 0.02;
e1 is a rational number of 0.0007 to 0.0015, preferably 0.0009 to 0.0015;
f1 is a rational number of 0.05 to 0.15, preferably 0.05 to 0.10; and
PLD4, NR4A1, KLRF1, ID3 and IL7R are, respectively, the expression levels of PLD4, NR4A1, KLRF1, ID3 and IL7R proteins or the genes encoding the proteins, measured in the biological sample isolated from the subject of interest.

In the present invention, the method of providing information may further comprise a step of substituting, into Equation 2 below, the expression levels of PLD4, ID3 and IL7R proteins or the genes encoding the proteins, measured in the biological sample isolated from the subject of interest:

$A = - a 2 - b 2 X (PLD 4) + c 2 X (IL) (7 R) + d 2 X (ID 3)$

wherein

a2 is a rational number of 0.5 to 0.9, preferably 0.70 to 0.85;
b2 is a rational number of 0.1 to 0.3, preferably 0.15 to 0.25;
c2 is a rational number of 0.0005 to 0.0025, preferably 0.001 to 0.002;
d2 is a rational number of 0.05 to 0.2, preferably a 0.10 to 0.15; and
PLD4, ID3 and IL7R are, respectively, the expression levels of PLD4, ID3 and IL7R proteins or the genes encoding the proteins, measured in the biological sample isolated from the subject of interest.

In the present invention, the values of PLD4, NR4A1, KLRF1, ID3 and IL7R, which are substituted into Equation 1 or 2 above, that is, the expression levels of the corresponding proteins or genes, may be normalized to the expression level of a housekeeping gene or a protein encoded by the housekeeping gene. Here, examples of the housekeeping gene include, but are not limited to, glyceraldehyde-3-phosphate desidrogenase (GAPDH), β-actin, ribosomal protein (RPL), ubiquitin (UBQ), β-tubulin, 18S ribosomal protein (18S rRNA), and phosphoglycerate kinase (PGK).
The method of providing information according to the present invention may further comprise a step of substituting the value obtained from Equation 1 or 2 above into Equation 3 below and predicting whether cancer has occurred or the likelihood of occurrence of cancer (Pr):

$\Pr = 1 / (1 + \exp (- A))$
In the present invention, when the value (Pr) obtained from Equation 3 above is greater than a rational number of 0.1 to 0.4, preferably 0.2 to 0.3, it may be predicted that cancer has occurred or is highly likely to occur.
In the method of providing information according to the present invention, predicting whether cancer has occurred or is highly likely to occur may comprise: predicting the likelihood of onset, growth, progression, or metastasis of cancer; predicting that a diseases that has occurred or is suspected of occurring in the subject of interest is cancer by distinguishing it from other diseases, in particular, pancreatic diseases (e.g., pancreatitis (including both acute and chronic), pancreatic benign tumors (lipoma or intraductal papillary mucinous neoplasm (IPMN), etc.); and predicting that cancer that has occurred or is suspected of occurring in the subject of interest is pancreatic cancer by distinguishing it from other cancer types.
In the present invention, the cancer may be thyroid cancer, parathyroid cancer, gastric cancer, ovarian cancer, colorectal cancer, pancreatic cancer, liver cancer, breast cancer, cervical cancer, lung cancer, non-small cell lung cancer, prostate cancer, gallbladder cancer, bile duct cancer, non-Hodgkin's lymphoma, Hodgkin's lymphoma, hematological cancer, bladder cancer, kidney cancer, melanoma, colon cancer, bone cancer, skin cancer, head cancer, uterine cancer, rectal cancer, brain tumor, perianal cancer, fallopian tube carcinoma, endometrial carcinoma, vaginal cancer, vulvar carcinoma, esophageal cancer, small intestine cancer, endocrine adenocarcinoma, adrenal cancer, soft tissue sarcoma, urethral cancer, penile cancer, cancer of ureter, renal cell carcinoma, renal pelvic carcinoma, central nervous system (CNS) tumor, primary CNS lymphoma, spinal cord tumor, brainstem glioma, or pituitary adenoma. Preferably, the cancer may be pancreatic cancer, but is not limited thereto and may be any type of cancer whose progression (such as tumor differentiation and/or proliferation) is dependent on the cancer cells or cancer stem cells described in the present invention.
The method of providing information according to the present invention further comprise a step of preventing, alleviating or treating cancer by administering an anticancer therapeutic drug to the subject of interest, when it is predicted that the cancer, preferably pancreatic cancer, has occurred or is highly likely to occur.
Here, the anticancer therapeutic drug may be, but is not limited to, at least one selected from the group consisting of nitrogen mustard, imatinib, oxaliplatin, rituximab, erlotinib, neratinib, lapatinib, gefitinib, vandetanib, nirotinib, semasanib, bosutinib, axitinib, masitinib, cediranib, restaurtinib, trastuzumab, gefitinib, bortezomib, sunitinib, pazopanib, toceranib, nintedanib, regorafenib, semaxanib, tivozanib, ponatinib, cabozantinib, carboplatin, sorafenib, lenvatinib, bevacizumab, cisplatin, cetuximab, viscum album, asparaginase, tretinoin, hydroxycarbamide, dasatinib, estramustine, gemtuzumab ozogamicin, ibritumomab tiuxetan, heptaplatin, methyl aminolevulinic acid, amsacrine, alemtuzumab, procarbazine, alprostadil, holmium nitrate chitosan, gemcitabine, doxifluridine, pemetrexed, tegafur, capecitabine, gimeracin, oteracil, azacitidine, methotrexate, uracil, cytarabine, 5-fluorouracil, fludarabine, enocitabine, flutamide, capecitabine, decitabine, mercaptopurine, thioguanine, cladribine, carmophor, raltitrexed, docetaxel, paclitaxel, irinotecan, belotecan, topotecan, vinorelbine, etoposide, vincristine, vinblastine, teniposide, doxorubicin, idarubicin, epirubicin, mitoxantrone, mitomycin, bleomycin, daunorubicin, dactinomycin, pirarubicin, aclarubicin, pepromycin, temsirolimus, busulfan, ifosfamide, cyclophosphamide, melphalan, altretamine, dacarbazine, thiotepa, nimustine, chlorambucil, mitolactol, leucovorin, tretonin, exemestane, amino glutesimide, anagrelide, olaparib, navelbine, fadrazole, tamoxifen, toremifene, testolactone, anastrozole, letrozole, vorozole, bicalutamide, lomustine, vorinostat, entinostat, and carmustine.
In the present invention, the anticancer therapeutic drug may be in the form of capsules, tablets, granules, injections, ointments, powders, or beverages, and the anticancer therapeutic drug may be for administration to humans.
For use, the anticancer therapeutic drug of the present invention may be formulated in the form of oral preparations such as powders, granules, capsules, tablets, and aqueous suspensions, preparations for external use, suppositories, and sterile injectable solutions, according to the respective conventional methods, without being limited thereto. The anticancer therapeutic drug of the present invention may further contain pharmaceutically acceptable carriers. As the pharmaceutically acceptable carriers, a binder, a lubricant, a disintegrant, an excipient, a solubilizer, a dispersant, a stabilizer, a suspending agent, a colorant, a flavoring agent, and the like may be used for oral administration; a buffer, a preservative, a pain-relieving agent, a solubilizer, an isotonic agent, a stabilizer, and the like may be used for injection; and a base, an excipient, a lubricant, a preservative, and the like may be used for topical administration. The pharmaceutical composition of the present invention may be prepared in various dosage forms by being mixed with the pharmaceutically acceptable carriers as described above. For example, for oral administration, the pharmaceutical composition may be formulated in the form of tablets, troches, capsules, elixirs, suspensions, syrups, wafers, or the like. For injection, the pharmaceutical composition may be formulated in the form of unit dosage ampoules or in multiple-dosage forms. In addition, the pharmaceutical composition may be formulated into solutions, suspensions, tablets, capsules, sustained-release preparations, or the like.
Meanwhile, examples of carriers, excipients and diluents suitable for formulation include lactose, dextrose, sucrose, sorbitol, mannitol, xylitol, erythritol, maltitol, starch, gum acacia, alginate, gelatin, calcium phosphate, calcium silicate, cellulose, methyl cellulose, microcrystalline cellulose, polyvinyl pyrrolidone, water, methylhydroxy benzoate, propylhydroxy benzoate, talc, magnesium stearate, and mineral oil. In addition, the pharmaceutical composition of the present invention may further contain a filler, an anticoagulant, a lubricant, a wetting agent, a fragrance, an emulsifier, a preservative, or the like.
The routes of administration of the anticancer therapeutic drug according to the present invention include, but are not limited to, oral, intravenous, intramuscular, intraarterial, intramedullary, intradural, intracardiac, transdermal, subcutaneous, intraperitoneal, intranasal, gastrointestinal, topical, sublingual and intrarectal routes. Oral or parenteral administration is preferred.
In the present invention, "parenteral" includes subcutaneous, transdermal, intravenous, intramuscular, intra-articular, intra-synovial, intrasternal, intradural, intralesional and intra-cranial injection or infusion techniques. The anticancer therapeutic drug of the present invention may also be formulated as suppositories for intrarectal administration.
The dose of the anticancer therapeutic drug of the present invention may vary depending on various factors, including the patient's age, body weight, general health status, sex, and diet, the time of administration, the route of administration, excretion rate, drug combination, and the severity of a particular disease to be prevented or treated. Although the dose of the anticancer therapeutic drug may vary depending on the patient's condition and body weight, the severity of the disease, the form of drug, and the route and duration of administration, it may be appropriately selected by those skilled in the art. The anticancer therapeutic drug may be administered at a dose of 0.0001 to 50 mg/kg/day or 0.001 to 50 mg/kg/day. The anticancer therapeutic drug may be administered once a day or several times a day. The dose does not limit the scope of the present invention in any way. The anticancer therapeutic drug according to the present invention may be formulated as pills, sugar-coated tablets, capsules, liquids, gels, syrups, slurries, or suspensions.

Advantageous Effects

By measuring the expression level of the biomarker protein or the gene encoding the biomarker protein according to the present invention, it is possible to accurately predict or diagnose whether cancer, particularly pancreatic cancer, has occurred or is likely to occur. In addition, according to the present invention, whether a disease has occurred may be predicted or diagnosed by measuring the expression level of the biomarker from a liquid biopsy isolated from a subject, and thus it is possible to diagnose cancer simply and rapidly, but very accurately, in a non-invasive way compared to a conventional art.

Brief Description of Drawings

FIG. 1 shows the results of analyzing the expressions level of PLD4 in peripheral blood mononuclear cells derived from a healthy control group and a pancreatic cancer patient group in Experimental Example 2, and an ROC curve for diagnosing pancreatic cancer based on the results.
FIG. 2 shows the results of analyzing the expressions level of NR4A1 in peripheral blood mononuclear cells derived from a healthy control group and a pancreatic cancer patient group in Experimental Example 2, and an ROC curve for diagnosing pancreatic cancer based on the results.
FIG. 3 shows the results of analyzing the expressions level of KLRF1 in peripheral blood mononuclear cells derived from a healthy control group and a pancreatic cancer patient group in Experimental Example 2, and an ROC curve for diagnosing pancreatic cancer based on the results.
FIG. 4 shows the results of analyzing the expressions level of IL7R in peripheral blood mononuclear cells derived from a healthy control group and a pancreatic cancer patient group in Experimental Example 2, and an ROC curve for diagnosing pancreatic cancer based on the results.
FIG. 5 shows the results of analyzing the expression levels of ID3 in peripheral blood mononuclear cells derived from a bile duct cancer patient group and a pancreatic cancer patient group in Experimental Example 3, and an ROC curve for diagnosing pancreatic cancer based on the results.
FIG. 6 shows ROC curves obtained by analyzing the scores of efficiency of pancreatic cancer diagnosis with a combination of five markers PLD4, NR4A1, KLRF1, ID3, and IL7R for a healthy control group and a pancreatic cancer patient group in Experimental Example 4.
FIG. 7 shows ROC curves obtained by analyzing the scores of efficiency of pancreatic cancer diagnosis with a combination of five markers PLD4, NR4A1, KLRF1, ID3, and IL7R for a benign pancreatic disease group and a pancreatic cancer patient group in Experimental Example 5.
FIG. 8 shows ROC curves obtained by analyzing the scores of efficiency of pancreatic cancer diagnosis with a combination of five markers PLD4, NR4A1, KLRF1, ID3, and IL7R for a high-risk group of pancreatic disease and a pancreatic cancer patient group in Experimental Example 5.

Best Mode

One embodiment of the present invention is directed to a biomarker for diagnosing cancer, preferably pancreatic cancer, comprising at least one protein selected from the group consisting of PLD4 (phospholipase D family member 4), NR4A1 (nuclear receptor subfamily 4 group A member 1), KLRF1 (killer cell lectin like receptor F1), and ID3 (inhibitor of DNA binding 3, HLH protein), or a gene encoding the at least one protein.
In the present invention, the biomarker may further comprise interleukin 7 receptor (IL7R) protein or a gene encoding the same.
In the present invention, the expression level of the biomarker, etc. may be measured from a biological sample isolated from a subject of interest, preferably cells or exosomes isolated from a liquid biopsy, for example, blood, serum or plasma.
In the present invention, the diagnosing may be predicting the likelihood of occurrence, growth, progression, or metastasis of cancer, or may be distinguishing cancer from other diseases, for example, pancreatic disease, in particular, pancreatitis (including both acute and chronic), pancreatic benign tumors (lipoma or intraductal papillary mucinous neoplasm (IPMN), etc.), or may be distinguishing between cancer types, particularly, distinguishing pancreatic cancer from other cancer types.

Mode for Invention

Hereinafter, the present invention will be described in detail with reference to the following examples. However, the following examples are only to illustrate the present invention, and the scope of the present invention is not limited by the following examples.

EXAMPLES

[Experimental Example 1]

In order to identify genes with significantly increased or decreased expression levels in peripheral blood mononuclear cells (PBMCs) obtained from a total of 23 individuals (a healthy control group (n = 8) and a pancreatic cancer (PDAC) patient group (n = 15)), mRNA-seq analysis (transcriptome sequencing) was performed as described below, and among about 350 genes significantly expressed in PBMCs of the pancreatic cancer patient group compared to the control group, a total of four biomarkers in Table 1 below were discovered and validated. In an experimental method, total RNA was isolated from the sample, and then DNA contamination was removed using DNase. Next, the RNA was purified using the TruSeq Stranded mRNA LT Sample Prep kit, and then randomly fragmented for sequencing with short reads. The cleaved RNA fragments were synthesized into cDNA through a reverse transcription process, and then different adapters were ligated to both ends of the cDNA fragment. Read sequencing from both ends of the cDNA fragment was performed. The raw reads obtained through this sequencing were subjected to a preprocessing process to reduce the deviation and then mapped to the reference genome using the HISAT2 program considering splices, and then aligned reads were generated. Using the reference-based aligned reads information, transcript assembly was performed through the StringTie program. The FPKM (Fragments Per Kilobase of transcript per Million mapped reads) or RPKM (Reads Per Kilobase of transcript per Million mapped reads) values, which are normalization values considering the read count, the transcript length and the depth of coverage, were calculated using the expression level obtained by the transcript quantification of each sample, thereby extracting expression profiles. Differentially expressed genes or transcripts were selected through statistical hypothesis validation of the expression values of two or more groups under different conditions. When there is known genetic information, functional annotation and gene-set enrichment analysis based on GO and KEGG databases was performed on differentially expressed genes.

[Table 1]

Gene_ID	Transcript_ID	Name		Fold
122618	NM_001308174,NM_138790	PLD4	phospholipase D family member 4	- 2.007829
3164	NM_001202233,NM_001202234,NM_00 2135,NM_173157	NR4A1	nuclear receptor subfamily 4 group A member 1	- 2.859995
51348	NM_001291822,NM_001291823,NM_001 366534,NM_016523	KLRF1	killer cell lectin like receptor F1	- 2.460315
3399	NM_002167	ID3	inhibitor of DNA binding 3, HLH protein	2.522447

As shown in Table 1, it could be confirmed that the mRNA expression levels of PLD4, NR4A1 and KLRF1 decreased in the pancreatic cancer patients compared to the healthy control group, whereas the mRNA expression level of ID3 increased.

[Experimental Example 2]

Peripheral blood mononuclear cells (PBMCs) were isolated from the blood of each of a healthy control group and a pancreatic cancer (PDAC) patient group, and then RNA was isolated therefrom (Qiagen, USA). Next, cDNA was synthesized from the RNA using a PrimeScript RT Master Mix (Perfect Real Time, Takara #RR036A). The mRNA expression levels of PLD4, NR4A1, KLRF1, and IL7R in each group were measured by performing PCR using a StepOnePlus PCR system (Applied Biosystems), and the results are shown in FIGS. 1 to 4. Primer sequences used in the PCR are shown in Table 2 below. In the following analysis, sensitivity indicates the probability that a person with a disease will show a positive outcome in diagnosis, specificity indicates the probability that a person without a disease will show a negative outcome in diagnosis, and AUC (Area Under the ROC Curve) is a measure for evaluating the performance of a predictor.

[Table 2]

Gene	Form	Sequence (5' -> 3')
PLD4 (Ref. NM_138790)	Forward primer	CAA ATT CTG GGT TGT GGA TGG
PLD4 (Ref. NM_138790)	Reverse primer	AGG TGG CTG CAG TTA TAG ATG
NR4A1 (Ref. NM_002135.5)	Forward primer	GACAACGCTTCATGCCAG
NR4A1 (Ref. NM_002135.5)	Reverse primer	TTGTTAGCCAGGCAGATGTAC
KLRF1 (Ref. NM_016523)	Forward primer	GAA AAG GAG TTC TGC CCA AAC
KLRF1 (Ref. NM_016523)	Reverse primer	AGA AAC CAA CAG GAT CAA GGA G
IL7R (Ref. NM_002185.5)	Forward primer	GTA GTC ATC ACT CCA GAA AGC
IL7R (Ref. NM_002185.5)	Reverse primer	ACC TGG AAG AGG AGA GAA TAG

As shown in FIGS. 1 to 4, it could be confirmed that the mRNA expression levels of PLD4, NR4A1 and KLRF1 significantly decreased (ΔCt increased) in the peripheral blood mononuclear cells (PBMCs) derived from the pancreatic cancer patient group compared to the healthy control group, the mRNA expression level of IL7R significantly increased (ΔCt decreased) in the peripheral blood mononuclear cells (PBMCs). In addition, it could be seen through the ROC curve that the accuracy of pancreatic cancer diagnosis was excellent when these biomarkers were used.

[Experimental Example 3]

Peripheral blood mononuclear cells (PBMCs) were isolated from the blood of each of a common bile duct (CBD) cancer patient group and a pancreatic cancer (PDAC) patient group, and then RNA was isolated therefrom (Qiagen, USA). Next, cDNA was synthesized from the RNA using a PrimeScript RT Master Mix (Perfect Real Time, Takara #RR036A). The mRNA expression level of ID3 in each group was measured by performing PCR using a StepOnePlus PCR system (Applied Biosystems), and the results are shown in FIG. 5. Primer sequences used in the PCR are shown in Table 3 below. [Table 3]

Gene Form Sequence (5' -> 3')

ID3 (Ref. NM_002167) Forward primer GAC TAC ATT CTC GAC CTG CAG

Reverse primer TCG TTG GAG ATG ACA AGT TCC
As shown in FIG. 5, it could be confirmed that the mRNA expression level of ID3 significantly increased (ΔCt decreased) in the peripheral blood mononuclear cells (PBMCs) derived from the pancreatic cancer patient group compared to the bile duct cancer patient group.

[Experimental Example 4]

Based on the results of Experimental Examples 2 and 3, the scores of efficiency of diagnosis with a combination of five markers PLD4, NR4A1, KLRF1, ID3, and IL7R to predict the healthy control group and the pancreatic cancer patient group were analyzed. SASSAS (version 9.3, SAS Inc., Cary, NC, USA) was used as the analysis software, and the following Equations 3 and 4 were derived by analyzing the predicted probability (Pr), and the ROC curve obtained by the analysis is shown in FIG 6. $\Pr = 1 / (1 + \exp (- A))$
$\begin{array}{l} A = 1.95710 - 0.21170 X (PLD 4) - 0.024072 X (NR 4 A 1) - \\ 0.012005 X (KLRF 1) + 0.00097174 X (IL) (7 R) + 0.086073 X (ID 3) \end{array}$
In Equation 4 above, PLD4, NR4A1, KLRF1, ID3, and IL7R are the mRNA expression levels (ΔCt values) of PLD4, NR4A1, KLRF1, ID3, and IL7R measured in the peripheral blood mononuclear cells of each group, respectively.
As a result, as shown in FIG. 6, as a result of analyzing the predicted probability (Pr) with a combination of five markers PLD4, NR4A1, KLRF1, ID3, and IL7R for prediction of the healthy control group and the pancreatic cancer patient group, it could be seen that the diagnostic accuracy (AUC) was 0.910, the sensitivity was 92.50%, and the specificity was 97.56%, which were all very high values, suggesting that, when the combination of five markers PLD4, NR4A1, KLRF1, ID3, and IL7R is used, whether pancreatic cancer has occurred or the likelihood of occurrence of pancreatic cancer can be predicted with excellent accuracy.

[Experimental Example 5]

Based on the results of Experimental Examples 2 and 3, the scores of efficiency of diagnosis with the combination of five markers PLD4, NR4A1, KLRF1, ID3 and IL7R were analyzed for diagnosis of the pancreatic cancer patient group versus a benign pancreatic disease group (acute pancreatitis and pancreatic lipoma) or a high-risk group of pancreatic disease (chronic pancreatitis and IPMN). SASSAS (version 9.3, SAS Inc., Cary, NC, USA) was used as the analysis software, and ROC curves obtained by the analysis are shown in FIGS. 7 and 8.
As shown in FIGS. 7 and 8, it was confirmed that the accuracy (AUC) of diagnosis of the pancreatic cancer patient group versus the benign pancreatic disease group (acute pancreatitis and pancreatic lipoma) with the combination of the five markers PLD4, NR4A1, KLRF1, ID3, and IL7R was 0.776 and the accuracy (AUC) of diagnosis of the pancreatic cancer patient group versus the high-risk group of pancreatic disease (chronic pancreatitis and IPMN) with the combination of the five markers was 0.789, suggesting that the combination of the five markers PLD4, NR4A1, KLRF1, ID3, and IL7R has significance as a biomarker for diagnosing pancreatic cancer by distinguishing it from other pancreatic diseases.

[Experimental Example 6]

Peripheral blood mononuclear cells (PBMC) were isolated from a total of 272 individuals (a pancreatic cancer (PDAC) patient group (n = 50) and a non-pancreatic cancer patient group (n = 222)) shown in Table 4 below, and then the expression levels of PLD4, ID3 and IL7R were measured using the primers for PLD4, ID3 and IL7R shown in Tables 2 and 3 above and the probes shown in Table 5 below. Next, in the same manner as in Experimental Examples 4 and 5, logistic regression models for PLD4, ID3, and IL7R markers alone or in combination were built as predictive models for distinguishing the pancreatic cancer patient group from the non-pancreatic cancer patient group. At this time, Equations 3 and 5 below were derived through predicted probability (Pr) analysis. The results of the analysis are shown in Tables 6 and 7 below. In Table 7 below, to determine the predictive power (area under the curve (AUC)) and diagnostic power (sensitivity, specificity, accuracy, PPV, NPV) of each model, the cut-off value was set as the point at which Youden's index (=sensitivity + specificity - 1) was maximized.

[Table 4]

	Patient groups
Pancreatic cancer patient group (n=50)		Non-pancreatic cancer patient group (n=222)
		- Normal persons (n=61)
		- High-risk group (chronic pancreatitis, pancreatic cyst, pancreatic duct dilatation, etc.) (n=56)
		- Benign pancreatic disease group (n=48)
		- Other digestive system cancer groups (bile duct cancer, gastric cancer, colorectal cancer, liver cancer, etc.) (n=54)
		- Others (n=3)

\Pr = 1 / (1 + \exp (- A))

A = - 0.789445 - 0.229438 X (PLD 4) + 0.001251 X (IL) (7 R) + 0.134571 X (ID 3)

In Equation 5, PLD4, ID3, and IL7R are, respectively, the ratios of the copy numbers of the PLD4, ID3 and IL7R markers to the GAPDH copy number (marker copy numbers/GAPDH copy number), measured for the peripheral blood mononuclear cells from each group.

[Table 5]

	Name	Sequence (5'-3')	Reporter 5'	Quencher 3'
1	PLD4-FAM	TCT GAC GCA GGT GAA GGA GCT TG	FAM	ZEN/IBFQ
2	IL7R-FAM	CAG TTG GAA GTG AAT GGA TCG CAG C	FAM	ZEN/IBFQ
3	ID3-FAM	CTC GGC TGT CTG GAT GGG AAG G	FAM	ZEN/IBFQ

[Table 6]

Variabl es	Single marker model					PLD4+ID3+IL7R combination marker model
Variabl es	Intercept	p-valu e	Beta (SE)	OR (95% CI)	p-valu e	Beta (SE)	OR (95% CI)	p-valu e	VIF
Interce pt	- 0.034331(0.3 140)	0.91 29	- 0.096451(0.0 208)	0.908(0.8 72-0.946)	<.00 01	- 0.229438(0.0 395)	0.795(0.7 36-0.859)	<.00 01	1.15 54
PLD4	- 2.165325(0.3 397)	<.00 01	0.000603(0.0 003)	1.001(1.0 00-1.001)	0.01 79	0.001251(0.0 004)	1.001(1.0 00-1.002)	0.00 25	1.68 04
IL7R	- 2.116365(0.2 716)	<.00 01	0.072584(0.0 237)	1.075(1.0 26-1.126)	0.00 22	0.134571(0.0 392)	1.144(1.0 59-1.235)	0.00 06	1.68 35
ID3	- 0.034331(0.3 140)	0.91 29	- 0.096451(0.0 208)	0.908(0.8 72-0.946)	<.00 01	- 0.229438(0.0 395)	0.795(0.7 36-0.859)	<.00 01	1.15 54

[Table 7]

Model	Optimal cut-off point	AUC (95% CI)	Sensitivity(95 % CI)	Specificity(9 5% CI)	Accuracy (95% CI)	PPV (95% CI)	NPV (95% CI)
PLD4	<18.8693	0.727(0.66 2-0.793)	0.900(0.817-0.983)	0.523(0.457-0.588)	0.592(0.53 4-0.650)	0.298(0.22 5-0.371)	0.959(0.92 3-0.994)
IL7R	>1025.40 733	0.621(0.53 3-0.709)	0.660(0.529-0.791)	0.568(0.502-0.633)	0.585(0.52 6-0.643)	0.256(0.18 1-0.331)	0.881(0.82 8-0.934)
ID3	>8.7021	0.640(0.54 3-0.737)	0.620(0.485-0.755)	0.716(0.657-0.776)	0.699(0.64 4-0.753)	0.330(0.23 5-0.425)	0.893(0.84 8-0.939)
PLD4+ID3 +IL7R	>0.22016	0.860(0.81 4-0.907)	0.840(0.738-0.942)	0.788(0.735-0.842)	0.798(0.75 0-0.846)	0.472(0.36 8-0.576)	0.956(0.92 7-0.986)

As a result, as shown in Tables 6 and 7 above, it was confirmed that the p-values of the regression coefficients of all the markers in the PLD4, IL7R, and ID3 single marker models in distinguishing pancreatic cancer from non-pancreatic cancer were less than 0.05, which were statistically significant, and that the p-values of the regression coefficients of the three markers in the multinomial logistic regression model of PLD4, IL7R, and ID3 built accordingly were also less than 0.05, which were statistically significant. In addition, it could be confirmed that the diagnostic accuracy (AUC), sensitivity, and specificity values were all high, and that these values became higher when the three markers were combined together.
This suggests that, when the single markers PLD4, IL7R, and ID3 and a combination thereof are used, it is possible to diagnose pancreatic cancer by distinguishing it from other diseases.
Although the present invention has been described in detail with reference to the specific features, it will be apparent to those skilled in the art that this description is only of a preferred embodiment thereof, and does not limit the scope of the present invention. Thus, the substantial scope of the present invention will be defined by the appended claims and equivalents thereto.

Industrial Applicability

Sequence Listing Free Text

Claims

A composition for diagnosing pancreatic cancer comprising, as an active ingredient, an agent for measuring an expression level of at least one protein selected from the group consisting of PLD4 (phospholipase D family member 4), NR4A1 (nuclear receptor subfamily 4 group A member 1), KLRF1 (killer cell lectin like receptor F1), and ID3 (inhibitor of DNA binding 3, HLH protein), or a gene encoding the at least one protein.
The composition according to claim 1, further comprising an agent for measuring an expression level of IL7R (interleukin 7 receptor) protein or a gene encoding the IL7R protein.
The composition according to claim 1, wherein the agent for measuring the expression level of the protein comprises at least one selected from the group consisting of an antibody, an oligopeptide, a ligand, a peptide nucleic acid (PNA), and an aptamer, which bind specifically to the protein.
The composition according to claim 1, wherein the agent for measuring the expression level of the gene comprises at least one selected from the group consisting of a primer, a probe, and an antisense nucleotide, which bind specifically to the gene.
The composition according to claim 1, wherein the composition is for a liquid biopsy isolated from a subject of interest.
The composition according to claim 1, wherein the composition is for predicting a likelihood of occurrence, growth, progression or metastasis of cancer, or for distinguishing between cancer and pancreatic disease, or for distinguishing between cancer types.
A kit for diagnosing pancreatic cancer comprising the composition according to any one of claims 1 to 6.
The kit according to claim 7, wherein the kit is an RT-PCR kit, a DNA chip kit, an ELISA kit, a protein chip kit, a rapid kit, or a multiple reaction monitoring (MRM) kit.
A method of providing information for diagnosis of pancreatic cancer, the method comprising a step of measuring an expression level of at least one protein selected from the group consisting of PLD4 (phospholipase D family member 4), NR4A1 (nuclear receptor subfamily 4 group A member 1), KLRF1 (killer cell lectin like receptor F1), and ID3 (inhibitor of DNA binding 3, HLH protein), or a gene encoding the at least one protein, in a biological sample isolated from a subject of interest.
The method according to claim 9, wherein the biological sample is at least one selected from the group consisting of whole blood, leukocytes, peripheral blood mononuclear cells, buffy coat, plasma, serum, sputum, tears, mucus, nasal washes, nasal aspirate, breath, urine, semen, saliva, peritoneal washings, ascites, cystic fluid, meningeal fluid, amniotic fluid, glandular fluid, pancreatic fluid, lymph fluid, pleural fluid, nipple aspirate, bronchial aspirate, synovial fluid, joint aspirate, organ secretions, cells, cell extracts, and cerebrospinal fluid.
The method according to claim 9, wherein the biological sample is a liquid biopsy.
The method according to claim 9, further comprising a step of measuring an expression level of IL7R protein or a gene encoding the IL7R protein in the biological sample isolated from the subject of interest.
The method according to claim 9, wherein the agent for measuring the expression level of the protein comprises at least one selected from the group consisting of an antibody, an oligopeptide, a ligand, a peptide nucleic acid (PNA), and an aptamer, which bind specifically to the protein.
The method according to claim 9, wherein the measuring the expression level of the protein is performed by protein chip assay, immunoassay, ligand binding assay, MALDI-TOF (Matrix Assisted Laser Desorption/Ionization Time of Flight) mass spectrometry, SELDI-TOF (Surface Enhanced Laser Desorption/Ionization Time of Flight) mass spectrometry, radioimmunoassay, radial immunodiffusion, Ouchterlony immunodiffusion, Rocket immunoelectrophoresis, immunohistostaining, complement fixation test, 2-D electrophoresis, liquid chromatography-mass spectrometry (LC-MS), liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS), Western blotting, enzyme-linked immunosorbent assay (ELISA), or a multiple reaction monitoring (MRM) method.
The method according to claim 9, wherein the agent for measuring the expression level of the gene comprises at least one selected from the group consisting of a primer, a probe, and an antisense nucleotide, which bind specifically to the gene.
The method according to claim 9, wherein the measuring the expression level of the gene is performed by reverse transcription polymerase reaction (RT-PCR), competitive RT-PCR, real-time RT-PCR, RNase protection assay (RPA), Northern blotting, or DNA chip assay.
The method according to claim 9, comprising predicting that pancreatic cancer has occurred or is highly likely to occur in the subject of interest, when the expression level of at least one protein selected from the group consisting of PLD4, NR4A1, and KLRF1, or the gene encoding the at least one protein, measured in the biological sample isolated from the subject of interest, is lower than a control.
The method according to claim 12, comprising predicting that pancreatic cancer has occurred or is highly likely to occur in the subject of interest, when the expression level of at least one protein selected from among ID3 and IL7R, or the gene encoding the protein, measured in the biological sample isolated from the subject of interest, is higher than a control.
The method according to claim 17 or 18, wherein the predicting that pancreatic cancer has occurred or is highly likely to occur comprises predicting a likelihood of occurrence, growth, progression or metastasis of pancreatic cancer, or distinguishing pancreatic cancer from pancreatic disease, or distinguishing pancreatic cancer from other cancer types.
A biomarker for diagnosing pancreatic cancer comprising at least one protein selected from the group consisting of PLD4 (phospholipase D family member 4), NR4A1 (nuclear receptor subfamily 4 group A member 1), KLRF1 (killer cell lectin like receptor F1), and ID3 (inhibitor of DNA binding 3, HLH protein), or a gene encoding the at least one protein.
The biomarker according to claim 20, further comprising IL7R (interleukin 7 receptor) protein or a gene encoding the IL7R protein.